galaxy-dev November 2011

galaxy-dev@lists.galaxyproject.org

83 participants
157 discussions

Galaxy Development Workshop: 23 January 2012, Český Krumlov, Czech Republic
by Dave Clements 11 Nov '11

11 Nov '11

Hello all, A one day Galaxy Developer Workshop<http://evomics.org/workshops/galaxy-developer-workshop/>has been scheduled for 23 January in Český Krumlov <http://www.ckrumlov.info/php/>, Czech Republic, immediately following the Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…>, (which also features Galaxy content, and is still taking applications). The Galaxy workshop is aimed at: - *IT and Bioinformatics staff:* - Galaxy is an easy to use, web-based tool that enables your researchers to perform data integration and analysis, in house, without handholding from you. This workshop will teach you how to install your own instance of Galaxy, either on your local compute infrastructure, or on the cloud. *Bioinformatics tool developers:* - Galaxy provides mechanisms for integrating your own tools and the tools of others into Galaxy instances. This workshop will cover how to define your tools in Galaxy, and how to then make those definitions available for installation in any Galaxy instance, thus making your tools much more accessible to the research community. This workshop also includes contributed talks from participants. If you have a topic of interest to the workshop’s audience, then please submit a short (500 words or less) abstract along with your registration<http://evomics.org/registration-form/galaxy-developer-workshop/>. Topics do not have to be directly related to Galaxy, but they should be of interest to those working with the integration, analysis, and sharing of large biological datasets. *15 December is the preferred registration deadline.* However, later registration will certainly be accepted dependent on availability. The registration fee is $200 USD (payment terms provided upon acceptance). Please forward this announcement on to any interested parties. Thanks, Dave C. PS: Plans for the 2012 Galaxy Community Conference<http://wiki.g2.bx.psu.edu/Events/GCC2012>are coming along nicely. Look for an announcement with dates soon. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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barcode splitter made 96 files. Is there a tool to map all of these files to the reference genome?
by Lucinda Lawson 11 Nov '11

11 Nov '11

Hi, I have Rad tag data that I'm trying to map to our reference genome in Galaxy on our local instance. After barcode splitter, I have 96 files (one each of all of the sequences for that individual). It seems like the current tools (e.g. bowtie) can only map a single file to the reference. I think that even if I were to do this step 96 times, I would still end up with 96 files at the end and not the linkage map that I hoped for. Any ideas on how to move forward from this stage? -Lucinda

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Velvetoptimizer won't read in my paired, illumina file
by Lucinda Lawson 11 Nov '11

11 Nov '11

Hi. I have an illumina 1.9 file that I renamed, groomed, and interlaced to get to its current state (see first 2 sets of paired sequences below) @1 TTTTTTATCAAAAAAAATGCATATACGAAATTTTTATTTTTACTTTTAAAAATTGAAAGTTGAAAATTTTAAATAAATGAAAAATAAATTAAACCAATTA +1 @CCCDDC?DDDFHHHGIIGJJIIIHEIJHGECIDHHHGIEGIGDHDGIHGHF4IGIHEGIJJJJIGHCFIJIHDHF4IIJIHHIGIGFHGHHFFFDF@@B @1 TTTATCAAAATATTTTCAAGCTAATTACAAGACATACTTACTTAAGTAAATTAAGATATATGGTTAATATTGCATTAAATAAGCTTTAATAAAGAGATAA +1 @CCDFFDFHHHGHJJJIIJJJIIIJJIIJIHIGGIBHGIHIHHIGIIIGHEIIICHGGHDHGIHHDIGIIGGGGICHGGDGFEG>EADECC7?CCDFD@C @2 ATTTATACATCTGTTGAACAAGTTATTAATTCTGTTTTCGATCTTTTTAATGTTATCTTTTACTTGTCCTCCCACATAGATCTTCATTCCTAAATTTATA +2 CCCC;,(>5(5((>3;AC>@@;3;?:DEHA;=A@55)((8)(6HGB8F?9<B?99)CHGGFCC?1)8)A+EC:CAA:F@FECA+B9C:BD4DDB2+;=+B @2 TATCCATACAAACTTATCATTCACTTTCAGTAGTAACCTATTCTTATTTTGTTTAACTTCAAATACCTTAAAAGGCCCTTCCCAAACACTATCTGACTTC +2 =8?;A=B?CFBBHGG2ACAC@@9E?F@HIIGHGI<+1?E9EEDHEC<GHBGHIGBFHCHFG@BB8BFFHCG:=;(=@D=C3?.;=;?DEC>C3>C(>>C> Now I want to do an initial assembly with velvetoptimizer on my local instance of Galaxy. When I run velvetoptimizer, calling this file a fastq file of short paired reads, it fails and I get this error message: SyntaxError: unexpected character after line continuation character Any ideas on what I'm doing wrong? Thanks! -Lucinda

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Adding bowtie-build ONLY as its own tool
by Nikhil Joshi 11 Nov '11

11 Nov '11

Hi all, So I am trying to add a tool to our local Galaxy, for which it needs a bowtie-build indexed reference, but NOT the alignment. The alignment step is done by the tool itself (using bowtie). My question is two-fold: One, why does the bowtie tool do both indexing and mapping? It seems that you would want to have the indexing separate from the alignment so that you can index once and then align as many times as you need. Right now it seems like (correct me if I am wrong) that EVERY time you do an alignment, Galaxy will index the reference. This seems like it is adding a lot more time to the alignment step than is necessary. Is this correct, or am I missing something? Two, so if I were to make bowtie-build into its own tool, how could I access the files that it creates, i.e. since bowtie-build takes a reference and a prefix as input and then creates multiple files that use the prefix.... I guess I need to access the prefix name somehow.... any help would be highly appreciated. Thanks! - Nik.

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Problem cutting files
by Elizabeth Ashley 11 Nov '11

11 Nov '11

Dear Galaxy users I am trying to cut a tab delimited file using the cut option under text manipulation. When the columns I wish are cut out, the resultant file contains only '.' (dots) where the data was in the previous file. Any ideas how to resolve this problem? Lizzy

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Deleting a Galaxy User
by Oren Livne 11 Nov '11

11 Nov '11

Dear All, Is it possible to delete a galaxy user or multiple users with a UI call or an API call? Thanks, Oren

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Error in log
by Chorny, Ilya 10 Nov '11

10 Nov '11

Our log is showing a strange error that does not seem to effect the way galaxy is behaving. Any thoughts? Thanks, Ilya f26d68045195cb8432494b6fbf HTTP/1.1" 200 - "-" "Python-urllib/2.6" galaxy.web.framework ERROR 2011-11-10 10:51:03,416 Uncaught exception in exposed API method: Traceback (most recent call last): File "/home/galaxy/production/Sept06/galaxy-central/lib/galaxy/web/framework/__init__.py", line 145, in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) File "/home/galaxy/production/Sept06/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py", line 268, in dumps use_decimal=use_decimal, **kw).encode(obj) File "/home/galaxy/production/Sept06/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/encoder.py", line 216, in encode chunks = list(chunks) File "/home/galaxy/production/Sept06/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/encoder.py", line 485, in _iterencode for chunk in _iterencode_dict(o, _current_indent_level): File "/home/galaxy/production/Sept06/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/encoder.py", line 439, in _iterencode_dict yield _encoder(value) UnicodeDecodeError: 'utf8' codec can't decode byte 0x93 in position 39: unexpected code byte Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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bug? workflow controller item slug for shared workflows
by Andrew Warren 10 Nov '11

10 Nov '11

Potential bug? I haven't seen any effects of this, and I don't really know whats going on with slugs, but I just wanted to mention it in case its an issue. Starting on line 149 of lib/galaxy/web/controllers/workflow.py there is a section of code for creating slugs for shared workflows. There is a loop there for slug creation and the following check OUTSIDE the loop: if slug_set: trans.sa_session.flush() Should that be in the loop? Otherwise its just flushing the session if the last workflow gets a slug created. -Andrew Warren

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Wrong smtplib exception
by Oleksandr Moskalenko 10 Nov '11

10 Nov '11

I have a diff for a bug that's been present in at least the last two releases of galaxy-dist when python 2.6(.5) is used, which doesn't have SMTPError in smtplib: --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -607,7 +607,7 @@ def send_mail( frm, to, subject, body, config ): log.error( "The server didn't accept the username/password combination: %s" % e ) s.close() raise - except smtplib.SMTPError, e: + except smtplib.SMTPException, e: log.error( "No suitable authentication method was found: %s" % e ) s.close() raise I had a problem with local instance of galaxy that could not send emails - error emails from the failed job history items for instance. When someone would submit the form they would get an error in the browser and no mail would come to the configured reporting address. Some debugging showed that lib/galaxy/util/__init__.py had a bug, which only surfaced because smtp_user = None smtp_password = None were uncommented in universe_wsgi.ini, which is strange in itself and could point to a bug in the universe configuration builder code as the corresponding code in lib/galaxy/util/__init__.py if config.smtp_username and config.smtp_password: should not be triggered by those uncommented entries. Regards, Alex

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Outputting zip files from galaxy
by wfmartin 10 Nov '11

10 Nov '11

I have an application that needs to return a zip file. I attempted to follow the instructions to add a "zip" datatype, with no success. It appears to me that Galaxy insists on generating the output file name and I can't get it to generate one with a ".zip" extension. The documentation on the wiki is missing a lot of details. Can you please point me to a working example of some code returning a zip file? Below are snippets of my code. Thanks, Bill Martin ================== tool_conf.xml: <toolbox> <section name="test" id="test_section_1"> <tool file="test/my_test.xml"/> </section> ================= tools/test/my_test.pl: #!/usr/bin/perl use strict; my ($output_1) = @ARGV; system("zip ${output_1} /home/bill/.* in.csv"); ===================== tools/test/my_test.xml: <tool id="my_test_1" name="my_test"> <description> the descr </description> <command interpreter="perl"> my_test.pl $output_1 </command> <inputs> <param format="tabular" name="input" type="data" label="inp" help="Dataset missing? See TIP below."/> </inputs> <outputs> <data format="zip" name="output_1"/> </outputs> </tool> =================== datatypes_conf.xml: <datatypes> <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> { some lines omitted here } <datatype extension="zip" type="galaxy.datatypes.binary:Zip" mimetype="application/zip" display_in_upload="true"/> { ... } </registration> ====================== lib/galaxy/datatypes/binary.py: { many lines omitted here } class Binary( data.Data ): """Binary data""" def set_peek( self, dataset, is_multi_byte=False ): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = 'binary data' dataset.blurb = 'data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def get_mime( self ): """Returns the mime type of the datatype""" return 'application/octet-stream' class Zip( Binary ): """Zip File""" file_ext = "zip" def get_mime( self ): """Returns the mime type of the datatype""" return 'application/zip' { many lines omitted here }

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galaxy-dev November 2011